R Notebook

library(tidyverse)
library(cowplot)
library(lubridate)
library(mgcv)
theme_set(theme_cowplot())
cb10 <- c('#a6cee3','#1f78b4','#b2df8a','#33a02c','#fb9a99','#e31a1c','#fdbf6f','#ff7f00','#cab2d6','#6a3d9a')

Particles Only

Read In Data

bes<- read_csv("dataOut/binned_EachSize.csv")

Parsed with column specification:
cols(
  .default = col_double(),
  project = col_character(),
  profile = col_character(),
  time = col_datetime(format = "")
)
See spec(...) for full column specifications.

bds <- read_csv("dataOut/binned_DepthSummary.csv")

Parsed with column specification:
cols(
  .default = col_double(),
  project = col_character(),
  profile = col_character(),
  time = col_datetime(format = "")
)
See spec(...) for full column specifications.

ues <- read_csv("dataOut/unbinned_EachSize.csv")

Parsed with column specification:
cols(
  project = col_character(),
  profile = col_character(),
  time = col_datetime(format = ""),
  depth = col_double(),
  psd_gam = col_double(),
  vol = col_double(),
  sizeclass = col_character(),
  lb = col_double(),
  ub = col_double(),
  binsize = col_double(),
  TotalParticles = col_double(),
  nparticles = col_double(),
  n_nparticles = col_double(),
  biovolume = col_double(),
  speed = col_double(),
  flux = col_double(),
  flux_fit = col_double(),
  GamPredictTP = col_double()
)

uds <- read_csv("dataOut/unbinned_DepthSummary.csv")

Parsed with column specification:
cols(
  .default = col_double(),
  project = col_character(),
  profile = col_character(),
  time = col_datetime(format = "")
)
See spec(...) for full column specifications.

Summary Statistics

PlotNParticles <- uds %>% 
  ggplot(aes(x = tot_nparticles, y = depth, col = profile)) +
 facet_wrap(~project) +
 geom_point(alpha = 0.3, shape = 1) +
scale_y_reverse() + scale_x_log10()

PlotNParticles

bdsAddTime <- bds %>%
  mutate(Hour = hour(time), Day = day(time))

FSG1 <- gam(tot_nparticles~ s(depth, k = 3) + s(Day, k = 3) + s(Hour, k = 4, bs = "cc"), knots = list(Hour = c(0, 24)), data = bdsAddTime %>% filter(depth >= 175 & depth <=500 & project == "ETNP"))

FSG2 <- gam(tot_nparticles ~ s(depth, k = 3) + s(Day, k = 3), data = bdsAddTime %>% filter(depth >= 175 & depth <=500 & project == "ETNP"))

FSG3 <- gam(tot_nparticles ~ s(depth, k = 3), data = bdsAddTime %>% filter(depth >= 175 & depth <=500 & project == "ETNP"))

#FSG4 <- gam(tot_nparticles~ s(depth, k = 3)  + s(Hour, k = 4, bs = "cc"), knots = list(Hour = c(0, 24)), data = bdsAddTime %>% filter(depth >= 175 & depth <=500 & project == "ETNP"))

summary(FSG1)

Family: gaussian 
Link function: identity 

Formula:
tot_nparticles ~ s(depth, k = 3) + s(Day, k = 3) + s(Hour, k = 4, 
    bs = "cc")

Parametric coefficients:
            Estimate Std. Error t value Pr(>|t|)    
(Intercept)    9.002      0.106   84.96   <2e-16 ***
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

Approximate significance of smooth terms:
           edf Ref.df     F p-value  
s(depth) 1.204  1.366 3.346  0.0874 .
s(Day)   1.512  1.761 3.001  0.0386 *
s(Hour)  1.579  2.000 2.713  0.0389 *
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

R-sq.(adj) =  0.183   Deviance explained = 24.2%
GCV = 0.73885  Scale est. = 0.67365   n = 60

#summary(FSG2)
#summary(FSG3)
#summary(FSG4)

summary(FSG1)$r.sq - summary(FSG2)$r.sq

[1] 0.07590024

summary(FSG2)$r.sq - summary(FSG3)$r.sq

[1] 0.05267319

summary(FSG3)$r.sq

[1] 0.0542546

But there is between projects:

ProjGam <- gam(tot_nparticles~ s(depth, k = 3) + factor(project), knots = list(Hour = c(0, 24)), data = bdsAddTime %>% filter(depth >= 175 & depth <=500))

summary(ProjGam)

Family: gaussian 
Link function: identity 

Formula:
tot_nparticles ~ s(depth, k = 3) + factor(project)

Parametric coefficients:
                   Estimate Std. Error t value Pr(>|t|)    
(Intercept)          8.9983     0.4445   20.24   <2e-16 ***
factor(project)P16  17.0001     1.3754   12.36   <2e-16 ***
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

Approximate significance of smooth terms:
         edf Ref.df     F p-value  
s(depth)   1      1 3.552   0.064 .
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

R-sq.(adj) =    0.7   Deviance explained = 70.9%
GCV = 12.411  Scale est. = 11.855    n = 67

PlotPSDmany <- uds %>% 
  filter(project == "ETNP") %>%
  ggplot(aes(x = psd, y = depth, shape = factor(day(time)), fill = hour(time))) +
 
  #geom_path(aes(x = psd_gam)) + 
  #geom_ribbon(aes(x = psd_gam, xmin = psd_gam - 2 * psd_seg, xmax = psd_gam + 2 * psd_seg), alpha = 0.1, outline_type = "lower") +
  geom_point(alpha = .6, size = 2, stroke = 1) +
  scale_y_reverse() + scale_shape_manual(values = c(21:25)) +
  scale_fill_gradientn(breaks = c(0, 6, 12, 18, 24), colors = c("black", "blue", "white", "orange", "black")) 

PlotParticlesmany <- uds %>% 
  filter(project == "ETNP") %>%
  ggplot(aes(x = tot_nparticles, y = depth, shape = factor(day(time)), fill = hour(time))) +
 
  #geom_path(aes(x = psd_gam)) + 
  #geom_ribbon(aes(x = psd_gam, xmin = psd_gam - 2 * psd_seg, xmax = psd_gam + 2 * psd_seg), alpha = 0.1, outline_type = "lower") +
  geom_point(alpha = .6, size = 2, stroke = 1) +
  scale_y_reverse() + scale_shape_manual(values = c(21:25)) +
  scale_fill_gradientn(breaks = c(0, 6, 12, 18, 24), colors = c("black", "blue", "white", "orange", "black")) +
  scale_x_log10() + theme(legend.position = "none")

PlotFluxmany <- uds %>% 
  filter(project == "ETNP") %>%
  ggplot(aes(x = tot_flux_fit, y = depth, shape = factor(day(time)), fill = hour(time))) +
 
  #geom_path(aes(x = psd_gam)) + 
  #geom_ribbon(aes(x = psd_gam, xmin = psd_gam - 2 * psd_seg, xmax = psd_gam + 2 * psd_seg), alpha = 0.1, outline_type = "lower") +
  geom_point(alpha = .6, size = 2, stroke = 1) +
  scale_y_reverse() + scale_shape_manual(values = c(21:25)) +
  scale_fill_gradientn(breaks = c(0, 6, 12, 18, 24), colors = c("black", "blue", "white", "orange", "black")) +
  scale_x_log10() + theme(legend.position = "none")



plot_grid(
  PlotParticlesmany,
  PlotPSDmany,
  rel_widths = c(2, 3)
  )

ggsave("figures/ParticlesPSDMany.png")

Saving 12 x 7.41 in image

ggsave("figures/ParticlesPSDMany.svg")

Saving 12 x 7.41 in image

bdsAddTime <- bds %>%
  mutate(Hour = hour(time), Day = day(time))

FSG1 <- gam(psd~ s(depth, k = 3) + s(Day, k = 3) + s(Hour, k = 4, bs = "cc"), knots = list(Hour = c(0, 24)), data = bdsAddTime %>% filter(depth >= 175 & depth <=500 & project == "ETNP"))

FSG2 <- gam(psd ~ s(depth, k = 3) + s(Day, k = 3), data = bdsAddTime %>% filter(depth >= 175 & depth <=500 & project == "ETNP"))

FSG3 <- gam(psd ~ s(depth, k = 3), data = bdsAddTime %>% filter(depth >= 175 & depth <=500 & project == "ETNP"))

FSG4 <- gam(psd~ s(depth, k = 3)  + s(Hour, k = 4, bs = "cc"), knots = list(Hour = c(0, 24)), data = bdsAddTime %>% filter(depth >= 175 & depth <=500 & project == "ETNP"))

summary(FSG1)

Family: gaussian 
Link function: identity 

Formula:
psd ~ s(depth, k = 3) + s(Day, k = 3) + s(Hour, k = 4, bs = "cc")

Parametric coefficients:
            Estimate Std. Error t value Pr(>|t|)    
(Intercept) -3.96083    0.01988  -199.3   <2e-16 ***
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

Approximate significance of smooth terms:
           edf Ref.df      F p-value    
s(depth) 1.713  1.917 56.197 5.5e-15 ***
s(Day)   1.000  1.000  1.078  0.3036    
s(Hour)  1.604  2.000  3.049  0.0285 *  
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

R-sq.(adj) =  0.635   Deviance explained = 66.1%
GCV = 0.026006  Scale est. = 0.023702  n = 60

#summary(FSG2)
#summary(FSG3)
summary(FSG4)

Family: gaussian 
Link function: identity 

Formula:
psd ~ s(depth, k = 3) + s(Hour, k = 4, bs = "cc")

Parametric coefficients:
            Estimate Std. Error t value Pr(>|t|)    
(Intercept) -3.96083    0.01995  -198.5   <2e-16 ***
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

Approximate significance of smooth terms:
           edf Ref.df      F  p-value    
s(depth) 1.715  1.919 55.141 7.66e-15 ***
s(Hour)  1.565  2.000  2.497   0.0488 *  
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

R-sq.(adj) =  0.632   Deviance explained = 65.2%
GCV = 0.02572  Scale est. = 0.023885  n = 60

summary(FSG1)$r.sq - summary(FSG2)$r.sq

[1] 0.03804023

summary(FSG2)$r.sq - summary(FSG3)$r.sq

[1] -0.004905911

summary(FSG3)$r.sq

[1] 0.6015425

Not a significant difference in PSD with respect to time.

But there is between projects:

ProjGam <- gam(psd~ s(depth, k = 3) + factor(project), knots = list(Hour = c(0, 24)), data = bdsAddTime %>% filter(depth >= 175 & depth <=500))

summary(ProjGam)

Family: gaussian 
Link function: identity 

Formula:
psd ~ s(depth, k = 3) + factor(project)

Parametric coefficients:
                   Estimate Std. Error  t value Pr(>|t|)    
(Intercept)        -3.96167    0.02491 -159.029   <2e-16 ***
factor(project)P16 -0.19977    0.07708   -2.592   0.0118 *  
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

Approximate significance of smooth terms:
           edf Ref.df     F  p-value    
s(depth) 1.224  1.398 34.54 2.26e-08 ***
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

R-sq.(adj) =  0.437   Deviance explained = 45.6%
GCV = 0.039117  Scale est. = 0.037234  n = 67

I wonder if I can show that the profiles aren’t statistically significanlty different. Or that they are for that matter… I think in that case, I run a gam with and without a parameter for profile… And then quantify the effect size of that parameter

Or follow this Gavin Simpson Post https://fromthebottomoftheheap.net/2017/10/10/difference-splines-i/

or anova.gam {mgcv}

Calculate gams for each profile, and then run anova.gam to see if they are different…

PlotNParticlesEP <- uds %>% 
  filter(profile %in% c("stn_043", "p16n_100")) %>%
  ggplot(aes(x = tot_nparticles, y = depth, col = project, shape = project)) +
 geom_point(alpha = 0.7, size = 2, stroke = 1) +
  #geom_path(aes(x = tot_nparticles)) +
  #geom_ribbon(aes(x = psd_gam, xmin = psd_gam - 2 * psd_seg, xmax = psd_gam + 2 * psd_seg), alpha = 0.1) +
scale_y_reverse(limits = c(2500, 0)) + scale_x_log10() + scale_color_manual(values = c("gray20", "brown")) +
  labs(x = "Particles/L", y = "depth (m)") +
  theme(legend.position = "none") +
  scale_shape_manual(values = c(1:5)) 

PlotNParticlesEP

I removed one outlyer from p16 for visualization purposes (300 particles/l at surface)

PlotPSDEP <- uds %>% 
  filter(profile %in% c("stn_043", "p16n_100")) %>%
  ggplot(aes(x = psd, y = depth, col = project, shape = project)) +
 geom_point(alpha = 0.7, size = 2, stroke = 1) +
  geom_path(aes(x = psd_gam)) +
  geom_ribbon(aes(x = psd_gam, xmin = psd_gam - 2 * psd_seg, xmax = psd_gam + 2 * psd_seg), alpha = 0.1) +
scale_y_reverse(limits = c(2500, 0)) + scale_color_manual(values = c("gray20", "brown"))  +
  scale_shape_manual(values = c(1:5)) + labs(y = "")

PlotPSDEP

I may just cow these togther.

plot_grid(PlotNParticlesEP, PlotPSDEP, rel_widths = c(2,3), labels = c("A", "B"))

Removed 611 rows containing missing values (geom_point).Removed 611 rows containing missing values (geom_point).Removed 611 row(s) containing missing values (geom_path).

ggsave("figures/ParticlesAndPSD_ETNPVsP16.svg")

Saving 10 x 4 in image

ggsave("figures/ParticlesAndPSD_ETNPVsP16.png")

Saving 10 x 4 in image

mainParticleComponents <- bds %>%
  filter(profile %in% c("stn_043", "p16n_100")) %>%
  select(project, profile, depth,
         tot_nparticles, small_nparticles, big_nparticles,
         tot_psd = psd, small_psd, big_psd,
         tot_flux_fit, small_flux_fit, big_flux_fit) %>%
  pivot_longer(cols = -c("project", "profile", "depth")) %>%
  separate(name, c("size", "meas")) %>%
  mutate(meas = recode(meas, nparticles = "particles/L")) %>%
  mutate(meas = factor(meas, levels = c("particles/L", "flux", "psd")))

Expected 2 pieces. Additional pieces discarded in 273 rows [7, 8, 9, 16, 17, 18, 25, 26, 27, 34, 35, 36, 43, 44, 45, 52, 53, 54, 61, 62, ...].

PlotFlx <- mainParticleComponents %>% 
  filter(meas != "psd") %>%
  ggplot(aes(y = depth, x = value, col = project, shape = project)) + facet_grid(size ~ meas, scales = "free_x") + geom_point(size = 2) + scale_y_reverse(limits = c(1000, 0)) + scale_x_log10() + theme(axis.title.x = element_blank(), legend.position = "none", strip.background.y = element_blank(), strip.text.y = element_blank(), plot.margin = unit(c(7,0,7,7), "pt")) + scale_color_manual(values = c("brown", "gray20")) + scale_shape_manual(values = c(1:5)) + theme(axis.text.x = element_text(angle = 90))

PlotPSD <- mainParticleComponents %>% 
  filter(meas == "psd") %>%
  ggplot(aes(y = depth, x = value, col = project, shape = project)) + facet_grid(size~meas, scales = "free_x") + geom_point(size = 2) + scale_y_reverse(limits = c(1000, 0)) +
  theme(axis.title.x = element_blank(), axis.title.y = element_blank(), axis.line.y = element_blank(), axis.text.y = element_blank(), axis.ticks.y = element_blank(), plot.margin = unit(c(7,7,26.5,0), "pt")) +
  scale_color_manual(values = c("brown", "gray20")) +  scale_shape_manual(values = c(1:5)) +  theme(axis.text.x = element_text(angle = 90))

plot_grid(PlotFlx, PlotPSD, rel_widths = c(3, 2))

Removed 246 rows containing missing values (geom_point).Removed 123 rows containing missing values (geom_point).

ggsave("figures/BigVsSmall.svg")

Saving 7.29 x 4.5 in image

ggsave("figures/BigVsSmall.png")

Saving 7.29 x 4.5 in image

Flux small and flux tot track so closely because ag > psd. since the size distribution of the flux sould be PSD + ag (psd is negative in this case). Yo ucan see the variance at the one depth where psd is flatest at the very top.

eg_dataline <- bds %>% 
  filter(profile == "stn_043", depth == 162.5)
eg_slope =  eg_dataline %>% pull(psd)
eg_icp = eg_dataline %>% pull(icp)
eg_vol = eg_dataline %>% pull(vol)

eg_datablock <- bes %>%
  filter(profile == "stn_043", depth == 162.5)


eg_lb = eg_datablock$lb
eg_binsize = eg_datablock$binsize
eg_nnp = exp(eg_icp + log(eg_lb) * eg_slope)

eg_np = eg_nnp * eg_binsize
eg_tp = eg_np * eg_vol
eg_df <- tibble(lb = eg_lb, n_nparticles = eg_nnp, nparticles = eg_np, TotalParticles = eg_tp)


EgNNP <- eg_datablock %>%
  ggplot(aes(x = lb, y = n_nparticles)) + geom_point() + scale_x_log10() + scale_y_log10() + 
  geom_path(data = eg_df) + labs(y = "Binsize & Volume Normalized \n Particles (#/L/mm)")

EgNP <- eg_datablock %>%
  ggplot(aes(x = lb, y = nparticles)) + geom_point() + scale_x_log10() + scale_y_log10() + 
  geom_path(data = eg_df) + labs(y = "Normalized Particles")

EgTP <- eg_datablock %>%
  ggplot(aes(x = lb, y = TotalParticles)) + geom_point() + scale_x_log10() + scale_y_log10() + 
  geom_path(data = eg_df) + labs( y = "Total Particles Observed (#)")

plot_grid(EgNNP, EgTP, labels = c("A", "B"))

Transformation introduced infinite values in continuous y-axisTransformation introduced infinite values in continuous y-axis

ggsave("figures/ExamplePSD163m.png")

Saving 7.29 x 4.5 in image

ggsave("figures/ExamplePSD163m.svg")

Saving 7.29 x 4.5 in image

Smooth flux and um disaggregation.

bds %>% 
  ggplot(aes(y = depth, x = Flux_Smooth, col = factor(time))) + facet_wrap(~project) + geom_point() + scale_y_reverse(limits = c(1000, 0)) + scale_x_log10()

bdsAddTime <- bds %>%
  mutate(Hour = hour(time), Day = day(time))

FSG1 <- gam(Flux_Smooth~ s(depth, k = 3) + s(Day, k = 3) + s(Hour, k = 4, bs = "cc"), knots = list(Hour = c(0, 24)), data = bdsAddTime %>% filter(depth >= 175 & depth <=500 & project == "ETNP"))

FSG2 <- gam(Flux_Smooth ~ s(depth, k = 3) + s(Day, k = 3), data = bdsAddTime %>% filter(depth >= 175 & depth <=500 & project == "ETNP"))

FSG3 <- gam(Flux_Smooth ~ s(depth, k = 3), data = bdsAddTime %>% filter(depth >= 175 & depth <=500 & project == "ETNP"))

summary(FSG1)

Family: gaussian 
Link function: identity 

Formula:
Flux_Smooth ~ s(depth, k = 3) + s(Day, k = 3) + s(Hour, k = 4, 
    bs = "cc")

Parametric coefficients:
            Estimate Std. Error t value Pr(>|t|)    
(Intercept)  34.7319     0.9334   37.21   <2e-16 ***
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

Approximate significance of smooth terms:
           edf Ref.df      F  p-value    
s(depth) 1.875  1.984 11.823 0.000126 ***
s(Day)   1.756  1.939  2.168 0.094012 .  
s(Hour)  1.114  2.000  1.658 0.059271 .  
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

R-sq.(adj) =   0.33   Deviance explained = 38.4%
GCV = 57.811  Scale est. = 52.277    n = 60

summary(FSG2)

Family: gaussian 
Link function: identity 

Formula:
Flux_Smooth ~ s(depth, k = 3) + s(Day, k = 3)

Parametric coefficients:
            Estimate Std. Error t value Pr(>|t|)    
(Intercept)  34.7319     0.9607   36.15   <2e-16 ***
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

Approximate significance of smooth terms:
           edf Ref.df      F  p-value    
s(depth) 1.869  1.983 11.102 0.000206 ***
s(Day)   1.811  1.964  2.743 0.094614 .  
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

R-sq.(adj) =   0.29   Deviance explained = 33.4%
GCV = 60.062  Scale est. = 55.377    n = 60

summary(FSG3)

Family: gaussian 
Link function: identity 

Formula:
Flux_Smooth ~ s(depth, k = 3)

Parametric coefficients:
            Estimate Std. Error t value Pr(>|t|)    
(Intercept)  34.7319     0.9944   34.93   <2e-16 ***
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

Approximate significance of smooth terms:
           edf Ref.df     F  p-value    
s(depth) 1.857  1.979 10.73 0.000277 ***
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

R-sq.(adj) =  0.239   Deviance explained = 26.3%
GCV = 62.291  Scale est. = 59.325    n = 60

summary(FSG1)$r.sq - summary(FSG2)$r.sq

[1] 0.03975922

summary(FSG2)$r.sq - summary(FSG3)$r.sq

[1] 0.05063133

summary(FSG3)$r.sq

[1] 0.2392424

bds %>% filter(project == "ETNP") %>% select(profile, depth, Flux_Smooth) %>% pivot_wider(names_from = profile, values_from = Flux_Smooth)

Something is off. All of the flux profiles are identical. Skip this

cb10 <- c('#a6cee3','#1f78b4','#b2df8a','#33a02c','#fb9a99','#e31a1c','#fdbf6f','#ff7f00','#cab2d6','#6a3d9a')
plt1 <- bds %>% #filter(DFP > 1) %>% #filter(profile %in% c("stn_043", "p16n_100")) %>%
  ggplot(aes(y = depth, x = DFP, col = factor(time), shape = factor(time))) + facet_wrap(~project) + geom_point() + scale_y_reverse(limits = c(1000, 0)) + xlim(c(0.5, 1.5))+ geom_vline(xintercept = 1) +
   scale_color_manual(values = c(rep("black", 5), rep("blue", 5))) + scale_shape_manual(values = rep(1:5, 2))

plotly::ggplotly(plt1)

What the heck is going on with DFP here. Why is it usually > 1 shouldn’t it be less than 1 when flux is decreasing? This very deep increasing flux seems improbable to me. Lets check the smooths. Or only go to 1000m.

cb10 <- c('#a6cee3','#1f78b4','#b2df8a','#33a02c','#fb9a99','#e31a1c','#fdbf6f','#ff7f00','#cab2d6','#6a3d9a')
pltFlx <- bds %>% #filter(DFP > 1) %>% #filter(profile %in% c("stn_043", "p16n_100")) %>%
  ggplot(aes(y = depth, x = Flux_Smooth, shape = factor(day(time)), fill = hour(time), group = factor(time))) + facet_wrap(~project) + geom_point(size = 3, stroke = 1)+
  geom_path() +
  scale_y_reverse(limits = c(2500, 0))+
  scale_x_log10() +
   scale_color_gradient2(low = "darkgreen", mid = "gray80", high = "purple", midpoint = 10) + scale_shape_manual(name = "Day of Month", values = rep(21:25, 2)) + 
  scale_fill_gradientn(name = "Hour of Day", breaks = c(0, 6, 12, 18, 24), colors = c("black", "blue", "white", "orange", "black")) +
  theme(axis.text.x = element_text(angle = 90)) +
labs(x = bquote(Smoothed~Flux~(µmol~C/m^2/d))) +
  geom_rect(data = data.frame(project = "ETNP"), aes(xmin = 20, xmax = 180, ymin = 75, ymax = 500), colour = "red", fill = NA, inherit.aes = FALSE)



pltFlxNoLegend <- pltFlx + theme(legend.position = "none")

pltFlx

#plotly::ggplotly(plt1)

cb10 <- c('#a6cee3','#1f78b4','#b2df8a','#33a02c','#fb9a99','#e31a1c','#fdbf6f','#ff7f00','#cab2d6','#6a3d9a')
pltFlxZoom <- bds %>% filter(project == "ETNP" & depth <= 500 & depth >= 75) %>% #filter(profile %in% c("stn_043", "p16n_100")) %>%
  ggplot(aes(y = depth, x = Flux_Smooth, shape = factor(day(time)), fill = hour(time), group = factor(time))) + geom_point(size = 3, stroke = 1)+
  geom_path() +
  scale_y_reverse()+
  #scale_x_log10() +
  scale_x_log10(breaks = c(seq(from = 20, to = 50, by = 10), seq(from = 60, to = 180, by = 20)), limits = c(20, 180)) +
   scale_color_gradient2(low = "darkgreen", mid = "gray80", high = "purple", midpoint = 10) + scale_shape_manual(values = rep(21:25, 2)) + 
  scale_fill_gradientn(breaks = c(0, 6, 12, 18, 24), colors = c("black", "blue", "white", "orange", "black")) +
  theme(axis.text.x = element_text(angle = 90)) +
labs(x = "Smoothed Flux") + theme(legend.position = "none")

pltFlxZoom

#plotly::ggplotly(plt1)

cb10 <- c('#a6cee3','#1f78b4','#b2df8a','#33a02c','#fb9a99','#e31a1c','#fdbf6f','#ff7f00','#cab2d6','#6a3d9a')
pltDelta3 <- bds %>% #filter(DFP > 1) %>% #filter(profile %in% c("stn_043", "p16n_100")) %>%
  ggplot(aes(y = depth, x = pracma::nthroot(DF/DZ, 5), shape = factor(day(time)), fill = hour(time), group = factor(time))) + facet_wrap(~project) + geom_point(size = 3, stroke = 1)+
  geom_path() +
  scale_y_reverse(limits = c(2500, 0))+
  scale_x_continuous(limits = c(-4.5, 1)) +
  #scale_x_log10() +
   scale_color_gradient2(low = "darkgreen", mid = "gray80", high = "purple", midpoint = 10) + scale_shape_manual(name = "Day of Month", values = rep(21:25, 2)) + 
  scale_fill_gradientn(name = "Hour", breaks = c(0, 6, 12, 18, 24), colors = c("black", "blue", "white", "orange", "black")) +
  geom_vline(xintercept = 0) +
  labs(x = bquote((DF/DZ)^{1/5}~(µmolC/m^3/d)^{1/5})) + theme(legend.pos = "none")
  #labs(x = "(DF/DZ) ^ 1/5 (µmol C/m^3/d) ^ 1/5")

pltDelta3

#plotly::ggplotly(plt1pos)

• theme(plot.margin = unit(c(0, 0, 0, 0), units = “cm”))

#plot_grid(pltFlxNoLegend, pltFlxZoom, pltDelta3, pltFlxLegend)

pltFlxLegend <- get_legend(pltFlx + theme(legend.box.margin = margin(0, 0, 40, 10)))

Removed 15 rows containing missing values (geom_point).Removed 15 row(s) containing missing values (geom_path).

pgTop <- plot_grid(pltFlxNoLegend, pltFlxZoom + theme(plot.margin = unit(c(1, 0, 3, 0), units = "cm")), rel_widths = c(2, 1), labels = c("A", "B"))

Removed 15 rows containing missing values (geom_point).Removed 15 row(s) containing missing values (geom_path).

pgBottom <- plot_grid(pltDelta3, pltFlxLegend , rel_widths = c(3, 1), labels = c("C", ""))

Removed 29 rows containing missing values (geom_point).Removed 29 row(s) containing missing values (geom_path).

pgBoth <- plot_grid(pgTop, pgBottom, ncol = 1)

pgBoth

ggsave("figures/FluxDeepDive.png")

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ggsave("figures/FluxDeepDive.svg")

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Test for day to day and hourly variability

bdsAddTime <- bds %>%
  mutate(Hour = hour(time), Day = day(time))

DFG1 <- gam(DF/DZ~ s(depth, k = 3) + s(Day, k = 3) + s(Hour, k = 4, bs = "cc"), knots = list(Hour = c(0, 24)), data = bdsAddTime %>% filter(depth >= 175 & depth <=500 & project == "ETNP"))

DFG2 <- gam(DF/DZ ~ s(depth, k = 3) + s(Day, k = 3), data = bdsAddTime %>% filter(depth >= 175 & depth <=500 & project == "ETNP"))

DFG3 <- gam(DF/DZ ~ s(depth, k = 3), data = bdsAddTime %>% filter(depth >= 175 & depth <=500 & project == "ETNP"))

summary(DFG1)

Family: gaussian 
Link function: identity 

Formula:
DF/DZ ~ s(depth, k = 3) + s(Day, k = 3) + s(Hour, k = 4, bs = "cc")

Parametric coefficients:
            Estimate Std. Error t value Pr(>|t|)    
(Intercept)  -0.1001     0.0171  -5.854 2.94e-07 ***
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

Approximate significance of smooth terms:
           edf Ref.df      F  p-value    
s(depth) 1.911  1.992 22.994 7.83e-08 ***
s(Day)   1.870  1.983  7.097  0.00126 ** 
s(Hour)  1.292  2.000  2.013  0.05235 .  
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

R-sq.(adj) =  0.514   Deviance explained = 55.5%
GCV = 0.019516  Scale est. = 0.017541  n = 60

summary(DFG2)

Family: gaussian 
Link function: identity 

Formula:
DF/DZ ~ s(depth, k = 3) + s(Day, k = 3)

Parametric coefficients:
            Estimate Std. Error t value Pr(>|t|)    
(Intercept) -0.10008    0.01769  -5.657 5.67e-07 ***
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

Approximate significance of smooth terms:
           edf Ref.df      F  p-value    
s(depth) 1.902  1.990 22.110 1.37e-07 ***
s(Day)   1.904  1.991  6.768  0.00339 ** 
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

R-sq.(adj) =  0.479   Deviance explained = 51.3%
GCV = 0.020417  Scale est. = 0.018782  n = 60

summary(DFG3)

Family: gaussian 
Link function: identity 

Formula:
DF/DZ ~ s(depth, k = 3)

Parametric coefficients:
            Estimate Std. Error t value Pr(>|t|)    
(Intercept) -0.10008    0.01944  -5.149 3.37e-06 ***
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

Approximate significance of smooth terms:
           edf Ref.df     F  p-value    
s(depth) 1.878  1.985 19.24 9.12e-07 ***
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

R-sq.(adj) =  0.371   Deviance explained = 39.1%
GCV = 0.023812  Scale est. = 0.02267   n = 60

summary(DFG1)$r.sq - summary(DFG2)$r.sq

[1] 0.03441623

summary(DFG2)$r.sq - summary(DFG3)$r.sq

[1] 0.1078441

summary(DFG3)$r.sq

[1] 0.3713016

plot(DFG1)

#Osps

(u mol C / m^3 / day)

bds %>% 
  ggplot(aes(y = depth, x = pracma::nthroot(ospsDZ, 3), shape = factor(day(time)), fill = hour(time), group = factor(time))) + facet_wrap(~project) + geom_point(size = 2) + scale_y_reverse(limits = c(2500, 0)) + geom_vline(xintercept = 0) +   scale_shape_manual(name = "Day of Month", values = rep(21:25, 2)) + labs(x = bquote("Flux Size Shift"~μmol/m^3/day)) +
  scale_fill_gradientn(name = "Hour of Day", breaks = c(0, 6, 12, 18, 24), colors = c("black", "blue", "white", "orange", "black"))

#ggsave("..figures/FluxSizeShift.svg"

 ggsave("figures/FluxSizeShift.png")

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 ggsave("figures/FluxSizeShift.svg")

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bdsAddTime <- bds %>%
  mutate(Hour = hour(time), Day = day(time))

OZG1 <- gam(ospsDZ ~ s(depth, k = 3) + s(Day, k = 3) + s(Hour, k = 4, bs = "cc"), knots = list(Hour = c(0, 24)), data = bdsAddTime %>% filter(depth >= 175 & depth <=500 & project == "ETNP"))

OZG2 <- gam(ospsDZ ~ s(depth, k = 3) + s(Day, k = 3), data = bdsAddTime %>% filter(depth >= 175 & depth <=500 & project == "ETNP"))

OZG3 <- gam(ospsDZ ~ s(depth, k = 3), data = bdsAddTime %>% filter(depth >= 175 & depth <=500 & project == "ETNP"))

summary(OZG1)

Family: gaussian 
Link function: identity 

Formula:
ospsDZ ~ s(depth, k = 3) + s(Day, k = 3) + s(Hour, k = 4, bs = "cc")

Parametric coefficients:
            Estimate Std. Error t value Pr(>|t|)    
(Intercept) 0.024817   0.002245   11.05 1.48e-15 ***
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

Approximate significance of smooth terms:
            edf Ref.df     F  p-value    
s(depth) 1.8892  1.988 8.422 0.000434 ***
s(Day)   1.8718  1.983 6.012 0.003119 ** 
s(Hour)  0.5513  2.000 0.396 0.243644    
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

R-sq.(adj) =  0.347   Deviance explained = 39.5%
GCV = 0.00033186  Scale est. = 0.00030248  n = 60

summary(OZG2)

Family: gaussian 
Link function: identity 

Formula:
ospsDZ ~ s(depth, k = 3) + s(Day, k = 3)

Parametric coefficients:
            Estimate Std. Error t value Pr(>|t|)    
(Intercept)  0.02482    0.00226   10.98 1.67e-15 ***
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

Approximate significance of smooth terms:
          edf Ref.df     F  p-value    
s(depth) 1.89  1.988 8.429 0.000428 ***
s(Day)   1.89  1.988 6.748 0.003790 ** 
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

R-sq.(adj) =  0.338   Deviance explained = 38.1%
GCV = 0.00033306  Scale est. = 0.00030653  n = 60

summary(OZG3)

Family: gaussian 
Link function: identity 

Formula:
ospsDZ ~ s(depth, k = 3)

Parametric coefficients:
            Estimate Std. Error t value Pr(>|t|)    
(Intercept) 0.024817   0.002479   10.01 3.55e-14 ***
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

Approximate significance of smooth terms:
           edf Ref.df     F  p-value    
s(depth) 1.872  1.984 7.338 0.000983 ***
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

R-sq.(adj) =  0.204   Deviance explained = 22.9%
GCV = 0.00038738  Scale est. = 0.00036884  n = 60

summary(OZG1)$r.sq - summary(OZG2)$r.sq

[1] 0.008753478

summary(OZG2)$r.sq - summary(OZG3)$r.sq

[1] 0.1344912

summary(OZG3)$r.sq

[1] 0.2038316

bds %>% filter(project == "P16") %>%
  ggplot(aes(y = depth, x = ospsDZ)) + facet_wrap(~project) + geom_point() + scale_y_reverse(limits = c(500, 0)) + geom_vline(xintercept = 0)

Trap data

trapFlux3 <- read_csv("dataOut/fluxMS_distilled.csv")

Parsed with column specification:
cols(
  Class = col_character(),
  Depth = col_double(),
  TrapID = col_character(),
  TrapType = col_character(),
  SampleType = col_character(),
  C_flux = col_double(),
  C_flux_umol = col_double()
)

UVPFluxComb <- read_csv("dataOut/CombinedProfileFluxEst_DS.csv")

Parsed with column specification:
cols(
  depth = col_double(),
  Flux = col_double()
)

trapFlux3

UVPFluxComb

binned_DepthSummary_ald_toPlot <- UVPFluxComb

fluxMS_distilled_toPlot <- trapFlux3 %>%
  mutate(SampleType = recode(SampleType, `plus.p` = "plus-particles", top = "top-collector"))

UVPFluxComb %>%
  ggplot(aes(y = depth))  + scale_y_reverse(limits = c(1000, 0)) +
  scale_x_continuous(limits = c(0, 200)) +
  geom_point(aes(y = Depth, x = C_flux_umol, fill = SampleType, shape = TrapType),
             colour = "black", stroke = 1, size = 5, data = fluxMS_distilled_toPlot) +
  geom_point(aes(x = Flux), size = 3, shape = 21, color = "white", fill = "black") +
  geom_point(aes(x = -1, y = -1, size = "UVP")) + # dummy point for the legend
scale_shape_manual(values = c(25, 22))+
  scale_size_manual(values = 1, name = "") +
  ylab("Depth (m)") + xlab("Flux µmolC/m^2/day") +
  guides(fill = guide_legend(override.aes = list(shape = 21))) +
  theme_cowplot() + 
  theme(
        legend.position = c(0.5, 0.4),
        legend.box.background = element_rect(color = "black", size = 0.5),
        legend.margin = margin(-10, 5, 10, 5)
  ) +
  geom_rect(data = data.frame(project = "ETNP"), aes(xmin = 15, xmax = 32, ymin = 45, ymax = 195), colour = "red", fill = NA, inherit.aes = FALSE)
ggsave("figures/FittedFlux.png")

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ggsave("figures/FittedFlux.svg")

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EK60

dataBinned <- read_csv("data/backscatter_table_go7.csv")

Parsed with column specification:
cols(
  frequency = col_double(),
  depth_bin = col_double(),
  time_bin = col_datetime(format = ""),
  value = col_double()
)

dataBinned_01 <- dataBinned %>%
  mutate(timeMex = with_tz(time_bin, tzone = "US/Central") )

startDay <- dataBinned_01$timeMex %>% na.omit %>% min %>% floor_date(unit = "days")
endDay <- dataBinned_01$timeMex %>% na.omit %>% max %>% ceiling_date(unit = "days")
timeBreaks <- seq(from = startDay, to = endDay, by = "12 hours")
timeLabels <- format(timeBreaks)

ggsave("figures/stationP2_EK60_18kOnly.svg")

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dataBinned_01 %>% ggplot(aes(x = timeMex, y = depth_bin, fill = value)) + geom_tile() + scale_y_reverse() + scale_fill_viridis_c(limits = c(-165, -75), oob = scales::squish) +
  scale_x_datetime(breaks = timeBreaks, date_labels = "%d::%H") + labs(x = "day::hour", y = "depth (m)", fill = "backscatter (dB)") + theme_bw() + theme(axis.text.x = element_text(angle = 90, vjust = 0.5)) +
  
  
  facet_wrap(~frequency, ncol = 1)

ggsave("figures/stationP2_EK60_go7.svg", width = 8, height = 20)